HEADER METAL BINDING PROTEIN 14-JAN-02 1KSO TITLE CRYSTAL STRUCTURE OF APO S100A3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: S100 CALCIUM-BINDING PROTEIN A3; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: S-100E PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: TB-1; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PMALC2; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMALC2-A3; SOURCE 10 EXPRESSION_SYSTEM_GENE: S100A3, S100E KEYWDS S100, EF-HAND, CA2+ BINDING PROTEIN, ZN2+ BINDING PROTEIN, METAL KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.R.MITTL,G.FRITZ,D.F.SARGENT,T.J.RICHMOND,C.W.HEIZMANN,M.G.GRUTTER REVDAT 6 14-FEB-24 1KSO 1 REMARK REVDAT 5 31-JAN-18 1KSO 1 REMARK REVDAT 4 01-FEB-17 1KSO 1 AUTHOR VERSN REVDAT 3 24-FEB-09 1KSO 1 VERSN REVDAT 2 01-APR-03 1KSO 1 JRNL REVDAT 1 31-JUL-02 1KSO 0 JRNL AUTH P.R.MITTL,G.FRITZ,D.F.SARGENT,T.J.RICHMOND,C.W.HEIZMANN, JRNL AUTH 2 M.G.GRUTTER JRNL TITL METAL-FREE MIRAS PHASING: STRUCTURE OF APO-S100A3. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 58 1255 2002 JRNL REFN ISSN 0907-4449 JRNL PMID 12136135 JRNL DOI 10.1107/S0907444902008430 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 594645.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 18292 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1800 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2578 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 304 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1510 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 199 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.96000 REMARK 3 B22 (A**2) : -1.96000 REMARK 3 B33 (A**2) : 3.92000 REMARK 3 B12 (A**2) : 0.18000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.17 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.630 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 4.640 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.520 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.510 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.880 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 51.40 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KSO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1000015302. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-01; 15-OCT-00 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.3 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; N REMARK 200 RADIATION SOURCE : ESRF; ROTATING ANODE REMARK 200 BEAMLINE : BM14; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; ENRAF-NONIUS FR571 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934; 1.5418 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18292 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS, AMMONIUM SULFATE, PH 8.3, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 20K, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 15.11267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.22533 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 SER A 95 REMARK 465 GLU A 96 REMARK 465 PRO A 97 REMARK 465 PRO A 98 REMARK 465 CYS A 99 REMARK 465 SER A 100 REMARK 465 GLN A 101 REMARK 465 MET B 1 REMARK 465 SER B 95 REMARK 465 GLU B 96 REMARK 465 PRO B 97 REMARK 465 PRO B 98 REMARK 465 CYS B 99 REMARK 465 SER B 100 REMARK 465 GLN B 101 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PRO A 94 O REMARK 470 PRO B 94 O REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 PRO A 94 CD REMARK 480 GLU B 49 CG CD OE1 OE2 REMARK 480 PRO B 94 CD REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU B 49 CB GLU B 49 CG -0.194 REMARK 500 REMARK 500 REMARK: NULL DBREF 1KSO A 1 101 UNP P33764 S10A3_HUMAN 1 101 DBREF 1KSO B 1 101 UNP P33764 S10A3_HUMAN 1 101 SEQRES 1 A 101 MET ALA ARG PRO LEU GLU GLN ALA VAL ALA ALA ILE VAL SEQRES 2 A 101 CYS THR PHE GLN GLU TYR ALA GLY ARG CYS GLY ASP LYS SEQRES 3 A 101 TYR LYS LEU CYS GLN ALA GLU LEU LYS GLU LEU LEU GLN SEQRES 4 A 101 LYS GLU LEU ALA THR TRP THR PRO THR GLU PHE ARG GLU SEQRES 5 A 101 CYS ASP TYR ASN LYS PHE MET SER VAL LEU ASP THR ASN SEQRES 6 A 101 LYS ASP CYS GLU VAL ASP PHE VAL GLU TYR VAL ARG SER SEQRES 7 A 101 LEU ALA CYS LEU CYS LEU TYR CYS HIS GLU TYR PHE LYS SEQRES 8 A 101 ASP CYS PRO SER GLU PRO PRO CYS SER GLN SEQRES 1 B 101 MET ALA ARG PRO LEU GLU GLN ALA VAL ALA ALA ILE VAL SEQRES 2 B 101 CYS THR PHE GLN GLU TYR ALA GLY ARG CYS GLY ASP LYS SEQRES 3 B 101 TYR LYS LEU CYS GLN ALA GLU LEU LYS GLU LEU LEU GLN SEQRES 4 B 101 LYS GLU LEU ALA THR TRP THR PRO THR GLU PHE ARG GLU SEQRES 5 B 101 CYS ASP TYR ASN LYS PHE MET SER VAL LEU ASP THR ASN SEQRES 6 B 101 LYS ASP CYS GLU VAL ASP PHE VAL GLU TYR VAL ARG SER SEQRES 7 B 101 LEU ALA CYS LEU CYS LEU TYR CYS HIS GLU TYR PHE LYS SEQRES 8 B 101 ASP CYS PRO SER GLU PRO PRO CYS SER GLN FORMUL 3 HOH *199(H2 O) HELIX 1 1 ARG A 3 GLY A 21 1 19 HELIX 2 2 GLN A 31 LEU A 42 1 12 HELIX 3 3 ARG A 51 ASN A 65 1 15 HELIX 4 4 ASP A 71 HIS A 87 1 17 HELIX 5 5 GLU A 88 LYS A 91 5 4 HELIX 6 6 ARG B 3 GLY B 21 1 19 HELIX 7 7 GLN B 31 LEU B 42 1 12 HELIX 8 8 ARG B 51 LEU B 62 1 12 HELIX 9 9 PHE B 72 HIS B 87 1 16 HELIX 10 10 GLU B 88 LYS B 91 5 4 SHEET 1 A 2 LEU A 29 CYS A 30 0 SHEET 2 A 2 GLU A 69 VAL A 70 -1 O VAL A 70 N LEU A 29 SHEET 1 B 2 LYS B 28 CYS B 30 0 SHEET 2 B 2 GLU B 69 ASP B 71 -1 O VAL B 70 N LEU B 29 CRYST1 58.769 58.769 45.338 90.00 90.00 120.00 P 31 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017016 0.009824 0.000000 0.00000 SCALE2 0.000000 0.019648 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022057 0.00000